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    CTNND2 catenin delta 2 [ Homo sapiens (human) ]

    Gene ID: 1501, updated on 29-Oct-2024

    Summary

    Official Symbol
    CTNND2provided by HGNC
    Official Full Name
    catenin delta 2provided by HGNC
    Primary source
    HGNC:HGNC:2516
    See related
    Ensembl:ENSG00000169862 MIM:604275; AllianceGenome:HGNC:2516
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GT24; NPRAP
    Summary
    This gene encodes an adhesive junction associated protein of the armadillo/beta-catenin superfamily and is implicated in brain and eye development and cancer formation. The protein encoded by this gene promotes the disruption of E-cadherin based adherens junction to favor cell spreading upon stimulation by hepatocyte growth factor. This gene is overexpressed in prostate adenocarcinomas and is associated with decreased expression of tumor suppressor E-cadherin in this tissue. This gene resides in a region of the short arm of chromosome 5 that is deleted in Cri du Chat syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013]
    Expression
    Biased expression in brain (RPKM 42.1) and spleen (RPKM 2.8) See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See CTNND2 in Genome Data Viewer
    Location:
    5p15.2
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (10971836..11904446, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (10909469..11841846, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (10971948..11904558, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized CTD-2154B17.1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15930 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:10761404-10762249 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:10904846-10905500 Neighboring gene death associated protein Neighboring gene DAP divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22383 Neighboring gene uncharacterized LOC105374654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10987709-10988210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22384 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:11022334-11023533 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:11065447-11066374 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:11069015-11069605 Neighboring gene RNA, U6 small nuclear 429, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr5:11141031-11141205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22385 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_80752 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:11385794-11386750 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:11466555-11466731 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:11528941-11529462 Neighboring gene NANOG hESC enhancer GRCh37_chr5:11700418-11700919 Neighboring gene NANOG hESC enhancer GRCh37_chr5:11797120-11797650 Neighboring gene Sharpr-MPRA regulatory region 1238 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:12237819-12238658 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:12320809-12321309 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:12321906-12322765 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:12322922-12323820 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:12323821-12324717 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:12330269-12331254 Neighboring gene uncharacterized LOC105374656 Neighboring gene uncharacterized LOC105374655 Neighboring gene RNA, U6 small nuclear 679, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2021-10-12)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2021-10-12)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
    EBI GWAS Catalog
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Genome-wide association studies reveal genetic variants in CTNND2 for high myopia in Singapore Chinese.
    EBI GWAS Catalog
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    EBI GWAS Catalog
    Genome-wide association study of lung function decline in adults with and without asthma.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables beta-catenin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables cadherin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in dendritic spine morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in dendritic spine morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in synapse organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in perikaryon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in postsynaptic density IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    catenin delta-2
    Names
    T-cell delta-catenin
    catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)
    neurojungin

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_023544.2 RefSeqGene

      Range
      4553..937163
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001288715.1NP_001275644.1  catenin delta-2 isoform 2

      See identical proteins and their annotated locations for NP_001275644.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding region, uses a downstream start codon, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AB013805, AC010626, AI680877, AK226124, DC332925, U52351, U52828
      Consensus CDS
      CCDS75228.1
      UniProtKB/TrEMBL
      A0A994J5I1, E7EPC8
      Related
      ENSP00000426510.1, ENST00000511377.5
      Conserved Domains (6) summary
      smart00185
      Location:490530
      ARM; Armadillo/beta-catenin-like repeats
      pfam00514
      Location:743784
      Arm; Armadillo/beta-catenin-like repeat
      sd00043
      Location:461486
      ARM; armadillo repeat [structural motif]
      cl25496
      Location:164292
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl27106
      Location:459632
      PLN03200; cellulose synthase-interactive protein; Provisional
      cl28033
      Location:72443
      Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
    2. NM_001288716.1NP_001275645.1  catenin delta-2 isoform 3

      See identical proteins and their annotated locations for NP_001275645.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding region, uses a downstream start codon, and lacks two alternate exons in the 5' coding region, compared to variant 1. The resulting protein (isoform 3) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC010626, AF035302, AI680877, AK299300, DB571461, DC332925
      Consensus CDS
      CCDS75227.1
      UniProtKB/TrEMBL
      B3KXF4, B4DJU1, B4DRK2
      Related
      ENSP00000426887.1, ENST00000503622.5
      Conserved Domains (4) summary
      smart00185
      Location:244284
      ARM; Armadillo/beta-catenin-like repeats
      PLN03200
      Location:213386
      PLN03200; cellulose synthase-interactive protein; Provisional
      sd00043
      Location:215240
      ARM; armadillo repeat [structural motif]
      pfam00514
      Location:288329
      Arm; Armadillo/beta-catenin-like repeat
    3. NM_001288717.2NP_001275646.1  catenin delta-2 isoform 4

      See identical proteins and their annotated locations for NP_001275646.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate internal exon and uses a downstream start codon, compared to variant 1. The resulting protein (isoform 4) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC010626, AC127460, AI680877, AK226124, AK296232, U52351, U52828
      UniProtKB/TrEMBL
      B3KXF4, B4DJU1
      Conserved Domains (4) summary
      smart00185
      Location:148188
      ARM; Armadillo/beta-catenin-like repeats
      PLN03200
      Location:117290
      PLN03200; cellulose synthase-interactive protein; Provisional
      sd00043
      Location:119144
      ARM; armadillo repeat [structural motif]
      pfam00514
      Location:401441
      Arm; Armadillo/beta-catenin-like repeat
    4. NM_001332.4NP_001323.1  catenin delta-2 isoform 1

      See identical proteins and their annotated locations for NP_001323.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
      Source sequence(s)
      AB013805, AC010626, AC127460, DC341093, U52351, U96136
      Consensus CDS
      CCDS3881.1
      UniProtKB/Swiss-Prot
      B0FTZ7, O00379, O15390, O43206, O43840, Q13589, Q9UM66, Q9UPM3, Q9UQB3
      Related
      ENSP00000307134.8, ENST00000304623.13
      Conserved Domains (5) summary
      smart00185
      Location:581621
      ARM; Armadillo/beta-catenin-like repeats
      pfam00514
      Location:834875
      Arm; Armadillo/beta-catenin-like repeat
      sd00043
      Location:552577
      ARM; armadillo repeat [structural motif]
      cl27106
      Location:550723
      PLN03200; cellulose synthase-interactive protein; Provisional
      cl28033
      Location:163534
      Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
    5. NM_001364128.2NP_001351057.1  catenin delta-2 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence, lacks two alternate exons, and contains another alternate in-frame exon compared to variant 1. The resulting isoform (6) is shorter at the N-terminus, lacks an alternate internal segment, and contains another alternate segment compared to isoform 1.
      Source sequence(s)
      AC003954, AC004648, AC005367, AC005610, AC010433, AC010626
      Consensus CDS
      CCDS93685.1
      UniProtKB/TrEMBL
      A0A994J5V2, B3KXF4, B4DJU1
      Related
      ENSP00000516315.1, ENST00000706271.1
      Conserved Domains (4) summary
      smart00185
      Location:244284
      ARM; Armadillo/beta-catenin-like repeats
      PLN03200
      Location:213386
      PLN03200; cellulose synthase-interactive protein; Provisional
      sd00043
      Location:215240
      ARM; armadillo repeat [structural motif]
      pfam00514
      Location:288329
      Arm; Armadillo/beta-catenin-like repeat

    RNA

    1. NR_109988.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC010626, AC127460, AK299300, DC341093, EU328348

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      10971836..11904446 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017009074.2XP_016864563.1  catenin delta-2 isoform X4

      UniProtKB/TrEMBL
      E9PHB5
      Conserved Domains (4) summary
      smart00185
      Location:335375
      ARM; Armadillo/beta-catenin-like repeats
      PLN03200
      Location:304477
      PLN03200; cellulose synthase-interactive protein; Provisional
      sd00043
      Location:306331
      ARM; armadillo repeat [structural motif]
      pfam00514
      Location:379420
      Arm; Armadillo/beta-catenin-like repeat
    2. XM_017009072.2XP_016864561.1  catenin delta-2 isoform X3

      UniProtKB/TrEMBL
      E9PHB5
      Related
      ENSP00000421093.1, ENST00000513588.5
      Conserved Domains (4) summary
      smart00185
      Location:335375
      ARM; Armadillo/beta-catenin-like repeats
      PLN03200
      Location:304477
      PLN03200; cellulose synthase-interactive protein; Provisional
      sd00043
      Location:306331
      ARM; armadillo repeat [structural motif]
      pfam00514
      Location:379420
      Arm; Armadillo/beta-catenin-like repeat
    3. XM_005248251.4XP_005248308.1  catenin delta-2 isoform X1

      See identical proteins and their annotated locations for XP_005248308.1

      Conserved Domains (4) summary
      cd00020
      Location:544666
      ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
      pfam00514
      Location:834875
      Arm; Armadillo/beta-catenin-like repeat
      pfam17052
      Location:10541113
      CAF20; Cap associated factor
      sd00043
      Location:552577
      ARM; armadillo repeat [structural motif]
    4. XM_011513967.3XP_011512269.1  catenin delta-2 isoform X2

      See identical proteins and their annotated locations for XP_011512269.1

      UniProtKB/TrEMBL
      A0A994J5I1
      Conserved Domains (4) summary
      cd00020
      Location:453575
      ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
      pfam00514
      Location:743784
      Arm; Armadillo/beta-catenin-like repeat
      pfam17052
      Location:9631022
      CAF20; Cap associated factor
      sd00043
      Location:461486
      ARM; armadillo repeat [structural motif]
    5. XM_005248253.2XP_005248310.1  catenin delta-2 isoform X2

      See identical proteins and their annotated locations for XP_005248310.1

      UniProtKB/TrEMBL
      A0A994J5I1
      Conserved Domains (4) summary
      cd00020
      Location:453575
      ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
      pfam00514
      Location:743784
      Arm; Armadillo/beta-catenin-like repeat
      pfam17052
      Location:9631022
      CAF20; Cap associated factor
      sd00043
      Location:461486
      ARM; armadillo repeat [structural motif]
    6. XM_047416777.1XP_047272733.1  catenin delta-2 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      10909469..11841846 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351724.1XP_054207699.1  catenin delta-2 isoform X4

    2. XM_054351723.1XP_054207698.1  catenin delta-2 isoform X3

    3. XM_054351719.1XP_054207694.1  catenin delta-2 isoform X1

    4. XM_054351720.1XP_054207695.1  catenin delta-2 isoform X6

    5. XM_054351722.1XP_054207697.1  catenin delta-2 isoform X2

    6. XM_054351721.1XP_054207696.1  catenin delta-2 isoform X2

    7. XM_054351725.1XP_054207700.1  catenin delta-2 isoform X5